Last updated: 2025-10-20
Checks: 5 2
Knit directory: PIPAC_spatial/
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| /home/hnatri/PIPAC_spatial/ | . |
| /home/hnatri/PIPAC_spatial/code/PIPAC_colors_themes.R | code/PIPAC_colors_themes.R |
| /home/hnatri/PIPAC_spatial/code/plot_functions.R | code/plot_functions.R |
| /home/hnatri/PIPAC_spatial/cell_main_cluster_marker_annotations.tsv | cell_main_cluster_marker_annotations.tsv |
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| html | 7c46eb3 | heinin | 2025-09-29 | Updated to denoised transcript data |
suppressPackageStartupMessages({
library(workflowr)
library(arrow)
library(Seurat)
library(SeuratObject)
library(SeuratDisk)
library(tidyverse)
library(tibble)
library(ggplot2)
library(ggpubr)
library(ggrepel)
library(googlesheets4)
library(workflowr)})
setwd("/home/hnatri/PIPAC_spatial/")
set.seed(9999)
options(scipen = 99999)
options(ggrepel.max.overlaps = Inf)
source("/home/hnatri/PIPAC_spatial/code/PIPAC_colors_themes.R")
source("/home/hnatri/PIPAC_spatial/code/plot_functions.R")
# Copied to isilon /tgen_labs/banovich/PIPAC/Seurat
# /tgen_labs/banovich/PIPAC/Seurat/cell_merged_spatial_filtered_splitsamples_clustered_NC50_NN20_PC20_Seurat.rds.rds
seurat_data <- readRDS("/tgen_labs/banovich/PIPAC/Seurat/cell_merged_spatial_filtered_splitsamples_clustered_NN30_PC50_Seurat_denoIST.rds")
head(seurat_data@meta.data)
orig.ident nCount_RNA nFeature_RNA
S21-24369_2A_TMA1_aaaafhkm-1_1 SeuratProject 34 22
S21-7951_5A_TMA1_aaabeech-1_1 SeuratProject 153 72
S21-7951_5A_TMA1_aaabidlm-1_1 SeuratProject 68 37
S21-7951_5A_TMA1_aaacanmk-1_1 SeuratProject 45 31
S21-7951_5A_TMA1_aaacnggd-1_1 SeuratProject 194 88
S21-7951_5A_TMA1_aaacoafb-1_1 SeuratProject 75 40
cell_id x_centroid
S21-24369_2A_TMA1_aaaafhkm-1_1 S21-24369_2A_TMA1_aaaafhkm-1_1 3120.635
S21-7951_5A_TMA1_aaabeech-1_1 S21-7951_5A_TMA1_aaabeech-1_1 3260.058
S21-7951_5A_TMA1_aaabidlm-1_1 S21-7951_5A_TMA1_aaabidlm-1_1 3167.581
S21-7951_5A_TMA1_aaacanmk-1_1 S21-7951_5A_TMA1_aaacanmk-1_1 3158.915
S21-7951_5A_TMA1_aaacnggd-1_1 S21-7951_5A_TMA1_aaacnggd-1_1 3176.202
S21-7951_5A_TMA1_aaacoafb-1_1 S21-7951_5A_TMA1_aaacoafb-1_1 3074.708
y_centroid transcript_counts
S21-24369_2A_TMA1_aaaafhkm-1_1 3213.421 34
S21-7951_5A_TMA1_aaabeech-1_1 5974.841 153
S21-7951_5A_TMA1_aaabidlm-1_1 6008.590 68
S21-7951_5A_TMA1_aaacanmk-1_1 6016.890 45
S21-7951_5A_TMA1_aaacnggd-1_1 6007.106 194
S21-7951_5A_TMA1_aaacoafb-1_1 5485.156 75
control_probe_counts genomic_control_counts
S21-24369_2A_TMA1_aaaafhkm-1_1 0 0
S21-7951_5A_TMA1_aaabeech-1_1 0 0
S21-7951_5A_TMA1_aaabidlm-1_1 0 0
S21-7951_5A_TMA1_aaacanmk-1_1 0 0
S21-7951_5A_TMA1_aaacnggd-1_1 0 0
S21-7951_5A_TMA1_aaacoafb-1_1 0 0
control_codeword_counts
S21-24369_2A_TMA1_aaaafhkm-1_1 0
S21-7951_5A_TMA1_aaabeech-1_1 0
S21-7951_5A_TMA1_aaabidlm-1_1 0
S21-7951_5A_TMA1_aaacanmk-1_1 0
S21-7951_5A_TMA1_aaacnggd-1_1 0
S21-7951_5A_TMA1_aaacoafb-1_1 0
unassigned_codeword_counts
S21-24369_2A_TMA1_aaaafhkm-1_1 0
S21-7951_5A_TMA1_aaabeech-1_1 0
S21-7951_5A_TMA1_aaabidlm-1_1 0
S21-7951_5A_TMA1_aaacanmk-1_1 0
S21-7951_5A_TMA1_aaacnggd-1_1 0
S21-7951_5A_TMA1_aaacoafb-1_1 0
deprecated_codeword_counts total_counts
S21-24369_2A_TMA1_aaaafhkm-1_1 0 34
S21-7951_5A_TMA1_aaabeech-1_1 0 153
S21-7951_5A_TMA1_aaabidlm-1_1 0 68
S21-7951_5A_TMA1_aaacanmk-1_1 0 45
S21-7951_5A_TMA1_aaacnggd-1_1 0 194
S21-7951_5A_TMA1_aaacoafb-1_1 0 75
cell_area nucleus_area nucleus_count
S21-24369_2A_TMA1_aaaafhkm-1_1 60.64485 33.68656 1
S21-7951_5A_TMA1_aaabeech-1_1 146.26110 32.06094 2
S21-7951_5A_TMA1_aaabidlm-1_1 75.36578 32.06094 1
S21-7951_5A_TMA1_aaacanmk-1_1 49.67188 18.78500 1
S21-7951_5A_TMA1_aaacnggd-1_1 126.75360 24.97141 1
S21-7951_5A_TMA1_aaacoafb-1_1 29.89344 14.90156 1
segmentation_method
S21-24369_2A_TMA1_aaaafhkm-1_1 Segmented by boundary stain (ATP1A1+CD45+E-Cadherin)
S21-7951_5A_TMA1_aaabeech-1_1 Segmented by boundary stain (ATP1A1+CD45+E-Cadherin)
S21-7951_5A_TMA1_aaabidlm-1_1 Segmented by boundary stain (ATP1A1+CD45+E-Cadherin)
S21-7951_5A_TMA1_aaacanmk-1_1 Segmented by boundary stain (ATP1A1+CD45+E-Cadherin)
S21-7951_5A_TMA1_aaacnggd-1_1 Segmented by boundary stain (ATP1A1+CD45+E-Cadherin)
S21-7951_5A_TMA1_aaacoafb-1_1 Segmented by boundary stain (ATP1A1+CD45+E-Cadherin)
num.blank TMA percent.blank
S21-24369_2A_TMA1_aaaafhkm-1_1 0 MR_PIPAC-TMA1 0
S21-7951_5A_TMA1_aaabeech-1_1 0 MR_PIPAC-TMA1 0
S21-7951_5A_TMA1_aaabidlm-1_1 0 MR_PIPAC-TMA1 0
S21-7951_5A_TMA1_aaacanmk-1_1 0 MR_PIPAC-TMA1 0
S21-7951_5A_TMA1_aaacnggd-1_1 0 MR_PIPAC-TMA1 0
S21-7951_5A_TMA1_aaacoafb-1_1 0 MR_PIPAC-TMA1 0
nCount_cell_RNA nFeature_cell_RNA Sample
S21-24369_2A_TMA1_aaaafhkm-1_1 34 22 S21-24369_2A
S21-7951_5A_TMA1_aaabeech-1_1 153 72 S21-7951_5A
S21-7951_5A_TMA1_aaabidlm-1_1 68 37 S21-7951_5A
S21-7951_5A_TMA1_aaacanmk-1_1 45 31 S21-7951_5A
S21-7951_5A_TMA1_aaacnggd-1_1 194 88 S21-7951_5A
S21-7951_5A_TMA1_aaacoafb-1_1 75 40 S21-7951_5A
leiden_0.5 leiden_1.0 leiden_1.5 leiden_2.0
S21-24369_2A_TMA1_aaaafhkm-1_1 9 10 13 16
S21-7951_5A_TMA1_aaabeech-1_1 3 6 2 7
S21-7951_5A_TMA1_aaabidlm-1_1 3 6 2 7
S21-7951_5A_TMA1_aaacanmk-1_1 3 6 2 7
S21-7951_5A_TMA1_aaacnggd-1_1 3 6 2 7
S21-7951_5A_TMA1_aaacoafb-1_1 5 26 7 33
Annotation Institution Patient_ID Timepoint
S21-24369_2A_TMA1_aaaafhkm-1_1 EpiTumor1 NWH S21-NWH-012 12
S21-7951_5A_TMA1_aaabeech-1_1 Meso NWH S21-NWH-011 0
S21-7951_5A_TMA1_aaabidlm-1_1 Meso NWH S21-NWH-011 0
S21-7951_5A_TMA1_aaacanmk-1_1 Meso NWH S21-NWH-011 0
S21-7951_5A_TMA1_aaacnggd-1_1 Meso NWH S21-NWH-011 0
S21-7951_5A_TMA1_aaacoafb-1_1 M8 NWH S21-NWH-011 0
Tissue Location_Quadrant RPN
S21-24369_2A_TMA1_aaaafhkm-1_1 Tumor Right Lower 012
S21-7951_5A_TMA1_aaabeech-1_1 Normal Unknown 011
S21-7951_5A_TMA1_aaabidlm-1_1 Normal Unknown 011
S21-7951_5A_TMA1_aaacanmk-1_1 Normal Unknown 011
S21-7951_5A_TMA1_aaacnggd-1_1 Normal Unknown 011
S21-7951_5A_TMA1_aaacoafb-1_1 Normal Unknown 011
STUDY_SITE GENDER
S21-24369_2A_TMA1_aaaafhkm-1_1 Northwell Health Cancer Institute Male
S21-7951_5A_TMA1_aaabeech-1_1 Northwell Health Cancer Institute Male
S21-7951_5A_TMA1_aaabidlm-1_1 Northwell Health Cancer Institute Male
S21-7951_5A_TMA1_aaacanmk-1_1 Northwell Health Cancer Institute Male
S21-7951_5A_TMA1_aaacnggd-1_1 Northwell Health Cancer Institute Male
S21-7951_5A_TMA1_aaacoafb-1_1 Northwell Health Cancer Institute Male
ETHNICITY race DISEASESITE
S21-24369_2A_TMA1_aaaafhkm-1_1 Non-Hispanic or Non-Latino Caucasian Appendiceal
S21-7951_5A_TMA1_aaabeech-1_1 Non-Hispanic or Non-Latino Caucasian Colorectal
S21-7951_5A_TMA1_aaabidlm-1_1 Non-Hispanic or Non-Latino Caucasian Colorectal
S21-7951_5A_TMA1_aaacanmk-1_1 Non-Hispanic or Non-Latino Caucasian Colorectal
S21-7951_5A_TMA1_aaacnggd-1_1 Non-Hispanic or Non-Latino Caucasian Colorectal
S21-7951_5A_TMA1_aaacoafb-1_1 Non-Hispanic or Non-Latino Caucasian Colorectal
ECOG ACTUALWEIGHT txstartdate
S21-24369_2A_TMA1_aaaafhkm-1_1 1 62.5 <NA>
S21-7951_5A_TMA1_aaabeech-1_1 0 86 <NA>
S21-7951_5A_TMA1_aaabidlm-1_1 0 86 <NA>
S21-7951_5A_TMA1_aaacanmk-1_1 0 86 <NA>
S21-7951_5A_TMA1_aaacnggd-1_1 0 86 <NA>
S21-7951_5A_TMA1_aaacoafb-1_1 0 86 <NA>
DXHISTOLOGY
S21-24369_2A_TMA1_aaaafhkm-1_1 8140/6-ADENOCARCINOMA, METASTATIC, NOS
S21-7951_5A_TMA1_aaabeech-1_1 8140/6-ADENOCARCINOMA, METASTATIC, NOS
S21-7951_5A_TMA1_aaabidlm-1_1 8140/6-ADENOCARCINOMA, METASTATIC, NOS
S21-7951_5A_TMA1_aaacanmk-1_1 8140/6-ADENOCARCINOMA, METASTATIC, NOS
S21-7951_5A_TMA1_aaacnggd-1_1 8140/6-ADENOCARCINOMA, METASTATIC, NOS
S21-7951_5A_TMA1_aaacoafb-1_1 8140/6-ADENOCARCINOMA, METASTATIC, NOS
DXSITE initialdxdate LINETHERAPY
S21-24369_2A_TMA1_aaaafhkm-1_1 C18.1-Appendix <NA> 2
S21-7951_5A_TMA1_aaabeech-1_1 C18.7-Sigmoid colon <NA> 4
S21-7951_5A_TMA1_aaabidlm-1_1 C18.7-Sigmoid colon <NA> 4
S21-7951_5A_TMA1_aaacanmk-1_1 C18.7-Sigmoid colon <NA> 4
S21-7951_5A_TMA1_aaacnggd-1_1 C18.7-Sigmoid colon <NA> 4
S21-7951_5A_TMA1_aaacoafb-1_1 C18.7-Sigmoid colon <NA> 4
PRIORTHERAPYTYPE priorcytoreduction
S21-24369_2A_TMA1_aaaafhkm-1_1 Chemotherapy, Multiple Agent 0
S21-7951_5A_TMA1_aaabeech-1_1 Chemotherapy, Single Agent NA
S21-7951_5A_TMA1_aaabidlm-1_1 Chemotherapy, Single Agent NA
S21-7951_5A_TMA1_aaacanmk-1_1 Chemotherapy, Single Agent NA
S21-7951_5A_TMA1_aaacnggd-1_1 Chemotherapy, Single Agent NA
S21-7951_5A_TMA1_aaacoafb-1_1 Chemotherapy, Single Agent NA
lastcontactdate furthertxall
S21-24369_2A_TMA1_aaaafhkm-1_1 <NA> Compassionate Use: PIPAC
S21-7951_5A_TMA1_aaabeech-1_1 <NA> <NA>
S21-7951_5A_TMA1_aaabidlm-1_1 <NA> <NA>
S21-7951_5A_TMA1_aaacanmk-1_1 <NA> <NA>
S21-7951_5A_TMA1_aaacnggd-1_1 <NA> <NA>
S21-7951_5A_TMA1_aaacoafb-1_1 <NA> <NA>
progressiondt vitalstatus1 deathdate
S21-24369_2A_TMA1_aaaafhkm-1_1 NA Alive <NA>
S21-7951_5A_TMA1_aaabeech-1_1 NA Alive <NA>
S21-7951_5A_TMA1_aaabidlm-1_1 NA Alive <NA>
S21-7951_5A_TMA1_aaacanmk-1_1 NA Alive <NA>
S21-7951_5A_TMA1_aaacnggd-1_1 NA Alive <NA>
S21-7951_5A_TMA1_aaacoafb-1_1 NA Alive <NA>
OFFSTUDYREASON
S21-24369_2A_TMA1_aaaafhkm-1_1 <NA>
S21-7951_5A_TMA1_aaabeech-1_1 Patient noncompliance after Week 14 - officially withdrew consent on 06AUG2021
S21-7951_5A_TMA1_aaabidlm-1_1 Patient noncompliance after Week 14 - officially withdrew consent on 06AUG2021
S21-7951_5A_TMA1_aaacanmk-1_1 Patient noncompliance after Week 14 - officially withdrew consent on 06AUG2021
S21-7951_5A_TMA1_aaacnggd-1_1 Patient noncompliance after Week 14 - officially withdrew consent on 06AUG2021
S21-7951_5A_TMA1_aaacoafb-1_1 Patient noncompliance after Week 14 - officially withdrew consent on 06AUG2021
offstudydate OFFTXREASON
S21-24369_2A_TMA1_aaaafhkm-1_1 <NA> Treatment Completed Per Protocol
S21-7951_5A_TMA1_aaabeech-1_1 <NA> Treatment Completed Per Protocol
S21-7951_5A_TMA1_aaabidlm-1_1 <NA> Treatment Completed Per Protocol
S21-7951_5A_TMA1_aaacanmk-1_1 <NA> Treatment Completed Per Protocol
S21-7951_5A_TMA1_aaacnggd-1_1 <NA> Treatment Completed Per Protocol
S21-7951_5A_TMA1_aaacoafb-1_1 <NA> Treatment Completed Per Protocol
offtxdate asascore1 asascore2 asascore3
S21-24369_2A_TMA1_aaaafhkm-1_1 <NA> ASA 3 ASA 3 ASA 3
S21-7951_5A_TMA1_aaabeech-1_1 <NA> ASA 3 ASA 3 ASA 3
S21-7951_5A_TMA1_aaabidlm-1_1 <NA> ASA 3 ASA 3 ASA 3
S21-7951_5A_TMA1_aaacanmk-1_1 <NA> ASA 3 ASA 3 ASA 3
S21-7951_5A_TMA1_aaacnggd-1_1 <NA> ASA 3 ASA 3 ASA 3
S21-7951_5A_TMA1_aaacoafb-1_1 <NA> ASA 3 ASA 3 ASA 3
lesionsize1 lesionsize2 lesionsize3 No_of_PIPACs
S21-24369_2A_TMA1_aaaafhkm-1_1 2 2 1 3
S21-7951_5A_TMA1_aaabeech-1_1 0 2 0 3
S21-7951_5A_TMA1_aaabidlm-1_1 0 2 0 3
S21-7951_5A_TMA1_aaacanmk-1_1 0 2 0 3
S21-7951_5A_TMA1_aaacnggd-1_1 0 2 0 3
S21-7951_5A_TMA1_aaacoafb-1_1 0 2 0 3
pipacdate1 pipacdate2 pipacdate3
S21-24369_2A_TMA1_aaaafhkm-1_1 YES YES YES
S21-7951_5A_TMA1_aaabeech-1_1 YES YES YES
S21-7951_5A_TMA1_aaabidlm-1_1 YES YES YES
S21-7951_5A_TMA1_aaacanmk-1_1 YES YES YES
S21-7951_5A_TMA1_aaacnggd-1_1 YES YES YES
S21-7951_5A_TMA1_aaacoafb-1_1 YES YES YES
ascites1
S21-24369_2A_TMA1_aaaafhkm-1_1 Large volume (>500 mL)
S21-7951_5A_TMA1_aaabeech-1_1 Small volume (<= 500 mL)
S21-7951_5A_TMA1_aaabidlm-1_1 Small volume (<= 500 mL)
S21-7951_5A_TMA1_aaacanmk-1_1 Small volume (<= 500 mL)
S21-7951_5A_TMA1_aaacnggd-1_1 Small volume (<= 500 mL)
S21-7951_5A_TMA1_aaacoafb-1_1 Small volume (<= 500 mL)
ascites2
S21-24369_2A_TMA1_aaaafhkm-1_1 Small volume (<= 500 mL)
S21-7951_5A_TMA1_aaabeech-1_1 Small volume (<= 500 mL)
S21-7951_5A_TMA1_aaabidlm-1_1 Small volume (<= 500 mL)
S21-7951_5A_TMA1_aaacanmk-1_1 Small volume (<= 500 mL)
S21-7951_5A_TMA1_aaacnggd-1_1 Small volume (<= 500 mL)
S21-7951_5A_TMA1_aaacoafb-1_1 Small volume (<= 500 mL)
ascites3 transfusion1
S21-24369_2A_TMA1_aaaafhkm-1_1 Small volume (<= 500 mL) None
S21-7951_5A_TMA1_aaabeech-1_1 Small volume (<= 500 mL) None
S21-7951_5A_TMA1_aaabidlm-1_1 Small volume (<= 500 mL) None
S21-7951_5A_TMA1_aaacanmk-1_1 Small volume (<= 500 mL) None
S21-7951_5A_TMA1_aaacnggd-1_1 Small volume (<= 500 mL) None
S21-7951_5A_TMA1_aaacoafb-1_1 Small volume (<= 500 mL) None
transfusion2 transfusion3 ebl1 ebl2 ebl3 pci1
S21-24369_2A_TMA1_aaaafhkm-1_1 None None 5 5 5 29
S21-7951_5A_TMA1_aaabeech-1_1 None None 20 20 5 14
S21-7951_5A_TMA1_aaabidlm-1_1 None None 20 20 5 14
S21-7951_5A_TMA1_aaacanmk-1_1 None None 20 20 5 14
S21-7951_5A_TMA1_aaacnggd-1_1 None None 20 20 5 14
S21-7951_5A_TMA1_aaacoafb-1_1 None None 20 20 5 14
pci2 pci3 numcycles_pipacsurg cyclenum age
S21-24369_2A_TMA1_aaaafhkm-1_1 28 24 3 3 61.6427
S21-7951_5A_TMA1_aaabeech-1_1 13 10 3 3 32.5749
S21-7951_5A_TMA1_aaabidlm-1_1 13 10 3 3 32.5749
S21-7951_5A_TMA1_aaacanmk-1_1 13 10 3 3 32.5749
S21-7951_5A_TMA1_aaacnggd-1_1 13 10 3 3 32.5749
S21-7951_5A_TMA1_aaacoafb-1_1 13 10 3 3 32.5749
lastfollowdate oscensor osmonths pfscensor
S21-24369_2A_TMA1_aaaafhkm-1_1 <NA> 1 17.9055 1
S21-7951_5A_TMA1_aaabeech-1_1 <NA> 1 4.4353 1
S21-7951_5A_TMA1_aaabidlm-1_1 <NA> 1 4.4353 1
S21-7951_5A_TMA1_aaacanmk-1_1 <NA> 1 4.4353 1
S21-7951_5A_TMA1_aaacnggd-1_1 <NA> 1 4.4353 1
S21-7951_5A_TMA1_aaacoafb-1_1 <NA> 1 4.4353 1
pfsmonths Arm SUBJECT_STATUS EXPIRED_DATE
S21-24369_2A_TMA1_aaaafhkm-1_1 17.9055 Arm2 <NA> <NA>
S21-7951_5A_TMA1_aaabeech-1_1 4.4353 Arm2 <NA> <NA>
S21-7951_5A_TMA1_aaabidlm-1_1 4.4353 Arm2 <NA> <NA>
S21-7951_5A_TMA1_aaacanmk-1_1 4.4353 Arm2 <NA> <NA>
S21-7951_5A_TMA1_aaacnggd-1_1 4.4353 Arm2 <NA> <NA>
S21-7951_5A_TMA1_aaacoafb-1_1 4.4353 Arm2 <NA> <NA>
race_oncore DOSELEVEL_STD HEIGHT COMMENTS500
S21-24369_2A_TMA1_aaaafhkm-1_1 <NA> <NA> <NA>
S21-7951_5A_TMA1_aaabeech-1_1 <NA> <NA> <NA>
S21-7951_5A_TMA1_aaabidlm-1_1 <NA> <NA> <NA>
S21-7951_5A_TMA1_aaacanmk-1_1 <NA> <NA> <NA>
S21-7951_5A_TMA1_aaacnggd-1_1 <NA> <NA> <NA>
S21-7951_5A_TMA1_aaacoafb-1_1 <NA> <NA> <NA>
PRIORHIPECYN furthertxdate No_of_PIPACS
S21-24369_2A_TMA1_aaaafhkm-1_1 <NA> <NA> <NA>
S21-7951_5A_TMA1_aaabeech-1_1 <NA> <NA> <NA>
S21-7951_5A_TMA1_aaabidlm-1_1 <NA> <NA> <NA>
S21-7951_5A_TMA1_aaacanmk-1_1 <NA> <NA> <NA>
S21-7951_5A_TMA1_aaacnggd-1_1 <NA> <NA> <NA>
S21-7951_5A_TMA1_aaacoafb-1_1 <NA> <NA> <NA>
priortherapytype1 agedx dxtosxmonths
S21-24369_2A_TMA1_aaaafhkm-1_1 <NA>
S21-7951_5A_TMA1_aaabeech-1_1 <NA>
S21-7951_5A_TMA1_aaabidlm-1_1 <NA>
S21-7951_5A_TMA1_aaacanmk-1_1 <NA>
S21-7951_5A_TMA1_aaacnggd-1_1 <NA>
S21-7951_5A_TMA1_aaacoafb-1_1 <NA>
sxtoendtxmonths sxtooffstudy cytoreduction
S21-24369_2A_TMA1_aaaafhkm-1_1 <NA>
S21-7951_5A_TMA1_aaabeech-1_1 <NA>
S21-7951_5A_TMA1_aaabidlm-1_1 <NA>
S21-7951_5A_TMA1_aaacanmk-1_1 <NA>
S21-7951_5A_TMA1_aaacnggd-1_1 <NA>
S21-7951_5A_TMA1_aaacoafb-1_1 <NA>
priorsxyn Site_abbr
S21-24369_2A_TMA1_aaaafhkm-1_1 <NA> S21-NWH
S21-7951_5A_TMA1_aaabeech-1_1 <NA> S21-NWH
S21-7951_5A_TMA1_aaabidlm-1_1 <NA> S21-NWH
S21-7951_5A_TMA1_aaacanmk-1_1 <NA> S21-NWH
S21-7951_5A_TMA1_aaacnggd-1_1 <NA> S21-NWH
S21-7951_5A_TMA1_aaacoafb-1_1 <NA> S21-NWH
unique(seurat_data$leiden_0.5)
[1] 9 3 5 14 16 11 6 17 1 8 0 10 12 2 13 15 4 7
DefaultAssay(seurat_data) <- "denoist_RNA"
DimPlot(seurat_data,
group.by = "leiden_0.5",
cols = pipac_cluster_20_col,
reduction = "umap",
raster = T,
label = T) +
coord_fixed(ratio = 1) +
theme_minimal() +
NoLegend()
| Version | Author | Date |
|---|---|---|
| 7c46eb3 | heinin | 2025-09-29 |
gs4_deauth()
metadata <- gs4_get("https://docs.google.com/spreadsheets/d/1sXXwOreLxjMSUoPt79c6jmaQpluWkaxA5P5HfDsed3I/edit?usp=sharing")
markers <- read_sheet(metadata, sheet = "Markers")
plot_features <- c("PTPRC",
"CD3D", "CD3E", "CD4", "CD8A", # T cells
"STAT4", "STAT3", "TIGIT", "GZMB",
"SELL", "CD19", # B cells
"CD68", "CD44", "MARCO", "APOE", # Macrophages
"C1QB", "C1QBP",
"MUC5AC", "NOTCH3", "MS4A1", "PGA5", # Lineage markers
"FN1", "DCN", "LUM", # Fibroblasts
"EGR3", "TP53", "JUN", "KIT", # Tumor
"SOX9", "RNF43", "EPCAM")
DotPlot(seurat_data,
group.by = "leiden_0.5",
features = plot_features,
cols = c("azure", "tomato3")) +
RotatedAxis()
| Version | Author | Date |
|---|---|---|
| 7c46eb3 | heinin | 2025-09-29 |
DefaultAssay(seurat_data) <- "RNA"
FeaturePlot(seurat_data,
slot = "data",
features = plot_features,
order = T,
ncol = 5,
reduction = "umap",
raster = T,
cols = c("gray89", "tomato3")) &
coord_fixed(ratio = 1) &
theme_bw() &
NoLegend()
| Version | Author | Date |
|---|---|---|
| 7c46eb3 | heinin | 2025-09-29 |
plot_features <- c("PTPRC",
"CD3D", "CD3E", "CD4", "CD8A", # T cells
"STAT4", "STAT3", "TIGIT", "GZMB",
"SELL", "CD19", # B cells
"CD68", "CD44", "MARCO", "APOE", # Macrophages
"C1QB", "C1QBP",
"MUC5AC", "NOTCH3", "MS4A1", "PGA5", # Lineage markers
"FN1", "DCN", "LUM", # Fibroblasts
"EGR3", "TP53", "JUN", "KIT", # Tumor
"SOX9", "RNF43", "EPCAM")
DefaultAssay(seurat_data) <- "denoist_RNA"
DotPlot(seurat_data,
group.by = "leiden_0.5",
features = plot_features,
cols = c("azure", "tomato3")) +
RotatedAxis()
FeaturePlot(seurat_data,
slot = "data",
features = plot_features,
order = T,
ncol = 5,
reduction = "umap",
raster = T,
cols = c("gray89", "tomato3")) &
coord_fixed(ratio = 1) &
theme_bw() &
NoLegend()
| Version | Author | Date |
|---|---|---|
| 7c46eb3 | heinin | 2025-09-29 |
Idents(seurat_data) <- seurat_data$leiden_0.5
cluster_markers <- FindAllMarkers(seurat_data,
return.thresh = 0.01,
logfc.threshold = 0.5,
min.pct = 0.20,
verbose = T)
table(cluster_markers$cluster)
9 3 5 14 16 11 6 17 1 8 0 10 12 2 13 15 4 7
134 89 115 54 42 60 98 74 20 86 84 71 68 60 53 22 50 56
hist(cluster_markers$avg_log2FC, main = "", xlab = "avg_log2FC", breaks = 100)
| Version | Author | Date |
|---|---|---|
| 7c46eb3 | heinin | 2025-09-29 |
hist(cluster_markers$p_val, main = "", xlab = "p_val", breaks = 100)
| Version | Author | Date |
|---|---|---|
| 7c46eb3 | heinin | 2025-09-29 |
hist(cluster_markers$p_val_adj, main = "", xlab = "p_val_adj", breaks = 100)
| Version | Author | Date |
|---|---|---|
| 7c46eb3 | heinin | 2025-09-29 |
top_cluster_markers <- cluster_markers %>%
arrange(dplyr::desc(avg_log2FC)) %>%
group_by(cluster) %>%
dplyr::slice(1:10)
create_dotplot_heatmap(seurat_object = seurat_data,
plot_features = unique(top_cluster_markers$gene),
group_var = "leiden_0.5",
group_colors = pipac_cluster_20_col,
column_title = "",
row_km = 5,
col_km = 5,
row.order = NULL,
col.order = NULL)
| Version | Author | Date |
|---|---|---|
| 7c46eb3 | heinin | 2025-09-29 |
output_cluster_markers <- cluster_markers %>%
arrange(dplyr::desc(avg_log2FC)) %>%
group_by(cluster) %>%
dplyr::slice(1:30)
output_cluster_markers <- merge(top_cluster_markers, markers, by.x = "gene", by.y = "Gene")
write.table(output_cluster_markers, "/home/hnatri/PIPAC_spatial/cell_main_cluster_marker_annotations.tsv",
quote = F, row.names = F, sep = "\t")
# Saving DenoIST top markers by original annotation
Idents(seurat_data) <- seurat_data$Annotation
cluster_markers <- FindAllMarkers(seurat_data,
return.thresh = 0.01,
logfc.threshold = 0.5,
min.pct = 0.20,
verbose = T)
output_cluster_markers <- cluster_markers %>%
arrange(dplyr::desc(avg_log2FC)) %>%
group_by(cluster) %>%
dplyr::slice(1:30)
output_cluster_markers <- merge(top_cluster_markers, markers, by.x = "gene", by.y = "Gene")
write.table(output_cluster_markers, "/home/hnatri/PIPAC_spatial/cell_annotation_top_markers.tsv",
quote = F, row.names = F, sep = "\t")
seurat_data$Lineage <- ifelse(seurat_data$leiden_0.5 %in% c(5, 6),
"Immune", "TumorStroma")
immune_subset <- subset(seurat_data, subset = Lineage == "Immune")
nonimmune_subset <- subset(seurat_data, subset = Lineage == "TumorStroma")
saveRDS(immune_subset, "/scratch/hnatri/PIPAC/cell_immune_subset.rds")
saveRDS(nonimmune_subset, "/scratch/hnatri/PIPAC/cell_nonimmune_subset.rds")
# To build on command line, run Rscript -e "rmarkdown::render('annotation_cell.Rmd')"
# Then "mv *.html /home/hnatri/PIPAC_spatial/docs/"
sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] ComplexHeatmap_2.18.0 viridis_0.6.3 viridisLite_0.4.2
[4] circlize_0.4.15 plyr_1.8.8 RColorBrewer_1.1-3
[7] googlesheets4_1.1.0 ggrepel_0.9.3 ggpubr_0.6.0
[10] lubridate_1.9.2 forcats_1.0.0 stringr_1.5.0
[13] dplyr_1.1.2 purrr_1.0.1 readr_2.1.4
[16] tidyr_1.3.0 tibble_3.2.1 ggplot2_3.4.2
[19] tidyverse_2.0.0 SeuratDisk_0.0.0.9021 Seurat_5.0.1
[22] SeuratObject_5.0.1 sp_1.6-1 arrow_21.0.0.1
[25] workflowr_1.7.1
loaded via a namespace (and not attached):
[1] RcppAnnoy_0.0.20 splines_4.3.0 later_1.3.1
[4] cellranger_1.1.0 polyclip_1.10-4 fastDummies_1.7.3
[7] lifecycle_1.0.3 rstatix_0.7.2 doParallel_1.0.17
[10] rprojroot_2.0.3 globals_0.16.2 processx_3.8.1
[13] lattice_0.21-8 hdf5r_1.3.8 MASS_7.3-60
[16] backports_1.4.1 magrittr_2.0.3 limma_3.58.1
[19] plotly_4.10.2 sass_0.4.6 rmarkdown_2.22
[22] jquerylib_0.1.4 yaml_2.3.7 httpuv_1.6.11
[25] sctransform_0.4.1 spam_2.9-1 spatstat.sparse_3.0-1
[28] reticulate_1.29 cowplot_1.1.1 pbapply_1.7-0
[31] abind_1.4-5 Rtsne_0.16 presto_1.0.0
[34] BiocGenerics_0.48.1 git2r_0.32.0 S4Vectors_0.40.2
[37] IRanges_2.36.0 irlba_2.3.5.1 listenv_0.9.0
[40] spatstat.utils_3.0-3 goftest_1.2-3 RSpectra_0.16-1
[43] spatstat.random_3.1-5 fitdistrplus_1.1-11 parallelly_1.36.0
[46] leiden_0.4.3 codetools_0.2-19 tidyselect_1.2.0
[49] shape_1.4.6 farver_2.1.1 stats4_4.3.0
[52] matrixStats_1.0.0 spatstat.explore_3.2-1 googledrive_2.1.0
[55] jsonlite_1.8.5 GetoptLong_1.0.5 ellipsis_0.3.2
[58] progressr_0.13.0 iterators_1.0.14 ggridges_0.5.4
[61] survival_3.5-5 foreach_1.5.2 tools_4.3.0
[64] ica_1.0-3 Rcpp_1.0.10 glue_1.6.2
[67] gridExtra_2.3 xfun_0.39 withr_2.5.0
[70] fastmap_1.1.1 fansi_1.0.4 callr_3.7.3
[73] digest_0.6.31 timechange_0.2.0 R6_2.5.1
[76] mime_0.12 colorspace_2.1-0 Cairo_1.6-0
[79] scattermore_1.2 tensor_1.5 spatstat.data_3.0-1
[82] utf8_1.2.3 generics_0.1.3 data.table_1.14.8
[85] httr_1.4.6 htmlwidgets_1.6.2 whisker_0.4.1
[88] uwot_0.1.14 pkgconfig_2.0.3 gtable_0.3.3
[91] lmtest_0.9-40 htmltools_0.5.5 carData_3.0-5
[94] dotCall64_1.0-2 clue_0.3-64 scales_1.2.1
[97] png_0.1-8 knitr_1.43 rstudioapi_0.14
[100] rjson_0.2.21 tzdb_0.4.0 reshape2_1.4.4
[103] nlme_3.1-162 curl_5.0.0 cachem_1.0.8
[106] zoo_1.8-12 GlobalOptions_0.1.2 KernSmooth_2.23-21
[109] parallel_4.3.0 miniUI_0.1.1.1 pillar_1.9.0
[112] vctrs_0.6.2 RANN_2.6.1 promises_1.2.0.1
[115] car_3.1-2 xtable_1.8-4 cluster_2.1.4
[118] evaluate_0.21 magick_2.7.4 cli_3.6.1
[121] compiler_4.3.0 rlang_1.1.1 crayon_1.5.2
[124] future.apply_1.11.0 ggsignif_0.6.4 labeling_0.4.2
[127] ps_1.7.5 getPass_0.2-4 fs_1.6.2
[130] stringi_1.7.12 deldir_1.0-9 assertthat_0.2.1
[133] munsell_0.5.0 lazyeval_0.2.2 spatstat.geom_3.2-1
[136] Matrix_1.6-5 RcppHNSW_0.5.0 hms_1.1.3
[139] patchwork_1.1.2 bit64_4.0.5 future_1.32.0
[142] statmod_1.5.0 shiny_1.7.4 highr_0.10
[145] ROCR_1.0-11 gargle_1.4.0 igraph_1.4.3
[148] broom_1.0.4 bslib_0.4.2 bit_4.0.5